OBJECTIVE: The detection of fetal aneuploidy and gene mutations by analysis of fetal cells in maternal blood has demonstrated the feasibility of noninvasive prenatal diagnosis. Fetal cells are rare in the maternal circulation; all current methods used for their isolation also yield maternal cells. We developed a method that permits a quantitative assessment of the relative numbers of fetal and maternal cells. STUDY DESIGN: Samples from 40 pregnant women were flow sorted with different monoclonal antibodies. Deoxyribonucleic acid was subsequently purified from candidate fetal cells; polymerase chain reaction was performed with synthetic primers specific for sequences on chromosomes Y and 7. RESULTS: The maximum number of fetal cells detected was 52 in 1080 maternal cells. Fetal cell purity ranged from 0.001% to 4.8%. Fetal cells were detected with antibodies to CD71, CD36, and glycophorin A. CONCLUSION: Quantitative polymerase chain reaction enables the determination of the purity and yield of fetal cells remaining after isolation from maternal blood, facilitating rapid comparisons between different cell separation techniques.